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ARID1A IDR Targets EWS-FLI1 Condensates and Finetunes Productive Chromatin Remodeling

GSE263234 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/01/08 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 12 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Topic
Ewing sarcomaThis series is part of our curated briefing on it.
Samples
12 samples: 6 conditions, mostly in duplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
ARID1A IDR targets EWS-FLI1 condensates and finetunes chromatin remodelingProtein & cell · 2025
Summary (written by the submitters)
The chimeric transcription factor EWS-FLI1 undergoes liquid-liquid phase separation (LLPS) and binds to neomorphic microsatellite DNA regions, which in turn recruits cBAF to activate an oncogenic transcriptional program in Ewing sarcoma. To identify the specific subunit of cBAF involved in this interaction, we employed unbiased TurboID analysis, revealing ARID1A as a potential mediator.
Read the full summary ↓
We discovered that an intrinsic disordered region of ARID1A, known as IDR1, undergoes homotypic phase separation and incorporates into EWS-FLI1 droplets. This finding suggests the direct involvement of IDR1 in recruiting cBAF to phase-separated EWS-FLI1. Additionally, we uncovered a surprising function of IDR1 in regulating the productive chromatin remodeling activity of cBAF. This novel discovery of ARID1A IDR1's dual role opens avenues for developing effective treatment strategies for relevant tumors.
Published in
ARID1A IDR targets EWS-FLI1 condensates and finetunes chromatin remodeling
Xue J, Lv S, Yu M et al. · Protein & cell 2025 · PMID 38761067 · doi:10.1093/procel/pwae029
This dataset
Open GSE263234 in finder → Find more human RNA-seq datasets → Ewing sarcoma landscape →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE263234_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1096325 and SRA study SRP499800. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38761067) ↗
Study design
6 conditions, mostly in duplicate
ARID1A-knockout 293T, O/E empty vector, O/E e… ×2 ARID1A-knockout 293T, O/E empty vector, O/E E… ×2 ARID1A-knockout 293T, O/E ARID1A WT, O/E empt… ×2 ARID1A-knockout 293T, O/E ARID1A WT, O/E EWS-… ×2 ARID1A-knockout 293T, O/E ARID1A ΔIDR1b, O/E … ×2 ARID1A-knockout 293T, O/E ARID1A ΔIDR1b, O/E … ×2

Supports a between-group comparison across 12 samples.

How we read this: 6 replicated groups read from 12 sample titles; they account for 12 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
More Ewing sarcoma datasets

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